Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 02:49:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/08_2023/7zyi_15024_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/08_2023/7zyi_15024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/08_2023/7zyi_15024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/08_2023/7zyi_15024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/08_2023/7zyi_15024_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/08_2023/7zyi_15024_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 46 5.16 5 Na 2 4.78 5 C 4286 2.51 5 N 1075 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 6641 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2248 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 14, 'TRANS': 278} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1714 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "K" Number of atoms: 930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Conformer: "B" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} bond proxies already assigned to first conformer: 931 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {' NA': 2, 'CHO': 2, 'CLR': 2} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Time building chain proxies: 4.28, per 1000 atoms: 0.64 Number of scatterers: 6641 At special positions: 0 Unit cell: (118.8, 116.82, 89.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 Na 2 11.00 O 1232 8.00 N 1075 7.00 C 4286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 12 sheets defined 30.0% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 22 through 45 removed outlier: 4.230A pdb=" N CYS A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 116 through 141 removed outlier: 4.098A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 156 through 179 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 181 through 212 removed outlier: 4.340A pdb=" N ARG A 185 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 200 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 285 through 309 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'H' and resid 107 through 109 removed outlier: 3.636A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.635A pdb=" N VAL H 182 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.599A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS H 200 " --> pdb=" O THR H 205 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.932A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.107A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'L' and resid 85 through 90 removed outlier: 3.601A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.636A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 144 through 150 removed outlier: 3.711A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.902A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA K 23 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL K 78 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.659A pdb=" N THR K 110 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1028 1.31 - 1.43: 1856 1.43 - 1.56: 3825 1.56 - 1.69: 19 1.69 - 1.81: 71 Bond restraints: 6799 Sorted by residual: bond pdb=" C12 CHO A 702 " pdb=" C13 CHO A 702 " ideal model delta sigma weight residual 1.529 1.198 0.331 2.00e-02 2.50e+03 2.73e+02 bond pdb=" C12 CHO A 703 " pdb=" C13 CHO A 703 " ideal model delta sigma weight residual 1.529 1.202 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C13 CHO A 702 " pdb=" C17 CHO A 702 " ideal model delta sigma weight residual 1.549 1.234 0.315 2.00e-02 2.50e+03 2.49e+02 bond pdb=" C13 CHO A 703 " pdb=" C17 CHO A 703 " ideal model delta sigma weight residual 1.549 1.242 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C11 CHO A 702 " pdb=" C12 CHO A 702 " ideal model delta sigma weight residual 1.529 1.812 -0.283 2.00e-02 2.50e+03 2.00e+02 ... (remaining 6794 not shown) Histogram of bond angle deviations from ideal: 94.96 - 102.76: 39 102.76 - 110.56: 1910 110.56 - 118.36: 3418 118.36 - 126.17: 3785 126.17 - 133.97: 99 Bond angle restraints: 9251 Sorted by residual: angle pdb=" CA PRO A 58 " pdb=" N PRO A 58 " pdb=" CD PRO A 58 " ideal model delta sigma weight residual 112.00 103.01 8.99 1.40e+00 5.10e-01 4.12e+01 angle pdb=" N MET A 229 " pdb=" CA MET A 229 " pdb=" CB MET A 229 " ideal model delta sigma weight residual 110.42 104.69 5.73 1.18e+00 7.18e-01 2.36e+01 angle pdb=" CA GLU H 46 " pdb=" CB GLU H 46 " pdb=" CG GLU H 46 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" CB MET A 229 " pdb=" CG MET A 229 " pdb=" SD MET A 229 " ideal model delta sigma weight residual 112.70 126.25 -13.55 3.00e+00 1.11e-01 2.04e+01 angle pdb=" CA LYS A 151 " pdb=" C LYS A 151 " pdb=" O LYS A 151 " ideal model delta sigma weight residual 120.90 116.14 4.76 1.07e+00 8.73e-01 1.98e+01 ... (remaining 9246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 3664 21.30 - 42.60: 277 42.60 - 63.91: 57 63.91 - 85.21: 7 85.21 - 106.51: 3 Dihedral angle restraints: 4008 sinusoidal: 1542 harmonic: 2466 Sorted by residual: dihedral pdb=" CA TYR A 183 " pdb=" C TYR A 183 " pdb=" N MET A 184 " pdb=" CA MET A 184 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C10 CHO A 702 " pdb=" C1 CHO A 702 " pdb=" C2 CHO A 702 " pdb=" C3 CHO A 702 " ideal model delta sinusoidal sigma weight residual 57.70 -48.81 106.51 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C10 CHO A 703 " pdb=" C1 CHO A 703 " pdb=" C2 CHO A 703 " pdb=" C3 CHO A 703 " ideal model delta sinusoidal sigma weight residual 57.70 -44.03 101.73 1 3.00e+01 1.11e-03 1.28e+01 ... (remaining 4005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 1065 0.331 - 0.662: 3 0.662 - 0.992: 0 0.992 - 1.323: 0 1.323 - 1.654: 2 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C13 CHO A 702 " pdb=" C12 CHO A 702 " pdb=" C14 CHO A 702 " pdb=" C17 CHO A 702 " both_signs ideal model delta sigma weight residual False -2.94 -1.29 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C13 CHO A 703 " pdb=" C12 CHO A 703 " pdb=" C14 CHO A 703 " pdb=" C17 CHO A 703 " both_signs ideal model delta sigma weight residual False -2.94 -1.30 -1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" C9 CHO A 703 " pdb=" C10 CHO A 703 " pdb=" C11 CHO A 703 " pdb=" C8 CHO A 703 " both_signs ideal model delta sigma weight residual False -2.52 -2.05 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 1067 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 107 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C LYS L 107 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS L 107 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG L 108 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 57 " 0.059 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 58 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 150 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C LEU A 150 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 150 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS A 151 " 0.015 2.00e-02 2.50e+03 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 142 2.70 - 3.25: 6147 3.25 - 3.80: 10105 3.80 - 4.35: 13056 4.35 - 4.90: 22655 Nonbonded interactions: 52105 Sorted by model distance: nonbonded pdb=" OD2 ASP K 97 " pdb=" OG SER K 100A" model vdw 2.152 2.440 nonbonded pdb=" OG SER L 182 " pdb=" OD2 ASP L 185 " model vdw 2.210 2.440 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.285 2.440 nonbonded pdb=" OG SER K 17 " pdb=" OD1 ASN K 82A" model vdw 2.311 2.440 nonbonded pdb=" NH1 ARG L 66 " pdb=" O GLY L 68 " model vdw 2.324 2.520 ... (remaining 52100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.480 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.820 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.331 6799 Z= 0.752 Angle : 0.754 13.548 9251 Z= 0.364 Chirality : 0.087 1.654 1070 Planarity : 0.005 0.084 1133 Dihedral : 15.699 106.510 2427 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 846 helix: 1.90 (0.33), residues: 260 sheet: 1.43 (0.35), residues: 211 loop : -0.41 (0.32), residues: 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 94 average time/residue: 1.1238 time to fit residues: 111.8659 Evaluate side-chains 91 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 1.8388 time to fit residues: 2.9452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 76 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100EGLN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 6799 Z= 0.239 Angle : 0.594 7.864 9251 Z= 0.298 Chirality : 0.043 0.277 1070 Planarity : 0.005 0.037 1133 Dihedral : 7.646 105.542 956 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 846 helix: 1.61 (0.32), residues: 261 sheet: 1.52 (0.34), residues: 219 loop : -0.55 (0.32), residues: 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 109 average time/residue: 1.0411 time to fit residues: 120.3359 Evaluate side-chains 105 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 9 residues processed: 9 average time/residue: 0.5794 time to fit residues: 6.6586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN H 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 6799 Z= 0.220 Angle : 0.555 6.281 9251 Z= 0.278 Chirality : 0.042 0.233 1070 Planarity : 0.005 0.037 1133 Dihedral : 7.658 104.361 956 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 5.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 846 helix: 1.57 (0.33), residues: 260 sheet: 1.61 (0.35), residues: 219 loop : -0.65 (0.31), residues: 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 0.721 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 111 average time/residue: 0.9874 time to fit residues: 116.6759 Evaluate side-chains 102 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.3517 time to fit residues: 3.8837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100EGLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 6799 Z= 0.239 Angle : 0.573 7.446 9251 Z= 0.284 Chirality : 0.042 0.238 1070 Planarity : 0.005 0.038 1133 Dihedral : 7.593 104.916 956 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 5.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 846 helix: 1.55 (0.33), residues: 260 sheet: 1.59 (0.35), residues: 219 loop : -0.75 (0.31), residues: 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 0.762 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 26 residues processed: 106 average time/residue: 1.0136 time to fit residues: 114.0921 Evaluate side-chains 111 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 15 residues processed: 11 average time/residue: 0.5235 time to fit residues: 7.2423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.2980 chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 6799 Z= 0.160 Angle : 0.513 5.983 9251 Z= 0.256 Chirality : 0.041 0.229 1070 Planarity : 0.004 0.038 1133 Dihedral : 7.373 101.568 956 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 5.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 846 helix: 1.72 (0.33), residues: 260 sheet: 1.62 (0.35), residues: 213 loop : -0.71 (0.31), residues: 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 111 average time/residue: 1.0129 time to fit residues: 119.4727 Evaluate side-chains 110 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 0.5607 time to fit residues: 4.6921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 16 optimal weight: 0.0470 chunk 47 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN L 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 6799 Z= 0.145 Angle : 0.515 8.281 9251 Z= 0.251 Chirality : 0.040 0.223 1070 Planarity : 0.004 0.037 1133 Dihedral : 7.261 101.376 956 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 4.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 846 helix: 1.79 (0.33), residues: 260 sheet: 1.60 (0.35), residues: 214 loop : -0.73 (0.31), residues: 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 110 average time/residue: 1.0036 time to fit residues: 117.4459 Evaluate side-chains 108 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 0.7317 time to fit residues: 5.6966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 59 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 6799 Z= 0.342 Angle : 0.634 6.596 9251 Z= 0.318 Chirality : 0.044 0.228 1070 Planarity : 0.005 0.045 1133 Dihedral : 7.711 104.951 956 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 5.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.29), residues: 846 helix: 1.39 (0.33), residues: 260 sheet: 1.54 (0.36), residues: 215 loop : -0.96 (0.30), residues: 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 90 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 115 average time/residue: 0.9776 time to fit residues: 119.6803 Evaluate side-chains 108 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.1130 time to fit residues: 1.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.0060 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6799 Z= 0.175 Angle : 0.541 8.441 9251 Z= 0.267 Chirality : 0.041 0.232 1070 Planarity : 0.004 0.036 1133 Dihedral : 7.374 100.343 956 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 846 helix: 1.64 (0.33), residues: 260 sheet: 1.50 (0.36), residues: 214 loop : -0.87 (0.30), residues: 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 108 average time/residue: 1.0091 time to fit residues: 115.8580 Evaluate side-chains 110 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 4 average time/residue: 0.1409 time to fit residues: 1.7525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 79 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 GLN L 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 6799 Z= 0.348 Angle : 0.641 6.540 9251 Z= 0.321 Chirality : 0.044 0.228 1070 Planarity : 0.005 0.044 1133 Dihedral : 7.653 104.223 956 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 4.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.29), residues: 846 helix: 1.36 (0.33), residues: 260 sheet: 1.37 (0.36), residues: 218 loop : -1.09 (0.30), residues: 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 89 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 111 average time/residue: 1.0631 time to fit residues: 125.1646 Evaluate side-chains 113 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.1205 time to fit residues: 2.2205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 6 optimal weight: 0.0030 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 GLN L 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6799 Z= 0.221 Angle : 0.558 6.169 9251 Z= 0.278 Chirality : 0.042 0.233 1070 Planarity : 0.005 0.036 1133 Dihedral : 7.415 100.964 956 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.29), residues: 846 helix: 1.78 (0.33), residues: 252 sheet: 1.39 (0.36), residues: 218 loop : -1.09 (0.30), residues: 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 113 average time/residue: 1.0453 time to fit residues: 125.7443 Evaluate side-chains 106 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 0.9879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.0370 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 GLN L 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.188382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126415 restraints weight = 22407.867| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.32 r_work: 0.3044 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6799 Z= 0.162 Angle : 0.530 6.267 9251 Z= 0.262 Chirality : 0.041 0.225 1070 Planarity : 0.004 0.036 1133 Dihedral : 7.206 99.691 956 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.29), residues: 846 helix: 1.90 (0.33), residues: 252 sheet: 1.41 (0.36), residues: 218 loop : -1.06 (0.30), residues: 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.68 seconds wall clock time: 51 minutes 6.40 seconds (3066.40 seconds total)